Change the color of a 3D image pixel and save it

Question

I have a 3D array. I want to change some pixel color of this 3D image. I want to change the pixel color for a given condition that is if my mask pixel for a fixed 3D co-ordinate is not equal 0 then I want to change my 3D array pixel to red color. Finally, I want to save this into a nifty format or .nii.gz format. I write some code this way, but this code gives me an error

  x, y, z=volume.shape
  for i in range (0, x):
     for j in range (0, y):
        for k in range (0, z):
           if(detections[i,j,k] !=0 ):
                volume[i ,j, k]=(255, 0, 0)
   ni_img = nib.Nifti1Image(output, volume.affine)
   nib.save(ni_img, '/content/SpineFinder-master/3d_path/output.nii.gz')



ValueError: setting an array element with a sequence volume[i, j, k]=(255, 0, 0)

How many dimensions does the volume have? I assume it's grayscale? — code-lukas, Aug 03 '20 at 10:01
Does this answer your question? [How to write a color 3D NIfTI with NiBabel?](https://stackoverflow.com/questions/40534333/how-to-write-a-color-3d-nifti-with-nibabel) — Christoph Rackwitz, Jun 10 '22 at 17:29

code-lukas · Answer 1 · 2020-08-06T11:17:35.570

0

The reason you are getting an error is because you can't 'just' write RGB values to nifti files. Please look up the question attached: How to write a color 3D NIfTI with NiBabel?

edited Aug 06 '20 at 11:17

answered Aug 03 '20 at 09:50

code-lukas

1,586
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score -1 · Answer 2 · answered Aug 03 '20 at 08:42

-1

I'd start with the missing comma (between i & j) in

volume[i j, k]=(255, 0, 0)

answered Aug 03 '20 at 08:42

Orius

1,093
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Sorry, this is a typo mistake when I write my question.I updated it. – Md. Abu Farhad Aug 03 '20 at 08:49

Change the color of a 3D image pixel and save it

2 Answers2